in‐vitro blood tests Search Results


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  • 99
    Thermo Fisher phytohemagglutinin
    IL-17A, IL-22 and proliferative responses from PBMCs obtained from healthy Swedish adults in response to stimulation with pneumococcal antigens. PBMCs were stimulated with the pneumococcal antigens WCA, PdT, PcsB, PsaA, the control antigens <t>PPD</t> and <t>PHA</t> or medium alone (NS) as described in the methods section. Five days after stimulation, the concentrations of IL-17A (A) and IL-22 (B) were measured in culture supernatants and cell proliferation was analyzed (C). Each symbol represents the responses from a single individual. Horizontal lines represent median responses.
    Phytohemagglutinin, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1761 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore sodium pyruvate
    IL-17A, IL-22 and proliferative responses from PBMCs obtained from healthy Swedish adults in response to stimulation with pneumococcal antigens. PBMCs were stimulated with the pneumococcal antigens WCA, PdT, PcsB, PsaA, the control antigens <t>PPD</t> and <t>PHA</t> or medium alone (NS) as described in the methods section. Five days after stimulation, the concentrations of IL-17A (A) and IL-22 (B) were measured in culture supernatants and cell proliferation was analyzed (C). Each symbol represents the responses from a single individual. Horizontal lines represent median responses.
    Sodium Pyruvate, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 16419 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher high capacity cdna reverse transcription kit
    Copy number of mtDNA and its transcription in the peripheral blood from diabetic subjects. ( a ) Copy number was quantified in the genomic <t>DNA</t> by qPCR using CYTB as mtDNA-encoded and β-ACTIN as a nuclear DNA-encoded gene. ( b ) Transcripts of mtDNA-encoded CYTB were quantified in the blood <t>cDNA</t> by qPCR using β-ACTIN as a housekeeping gene. The values are represented as mean ± SD obtained from five to six diabetic patients each with retinopathy (Diab-Ret) or without retinopathy (Diab-No Ret), and 7 to 10 nondiabetic subjects (Norm). * P
    High Capacity Cdna Reverse Transcription Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 119667 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher ion pgm system
    Comparison of matched genomic and cell-line transformed <t>DNA</t> for identified SNPs. Comparison of matched genomic and cell-line transformed DNA for rs141067872, rs10132942 (both miR - 329 - 2 ), rs7521574 and rs112695918 (both miR - 429 ) data generated by the Ion <t>PGM™.</t> The matching gDNA and cell-line transformed DNA show consistent results indicated by the base colour patterns in each example. Chr chromosome, hg human genome
    Ion Pgm System, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1135 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher knockout serum replacement ksr
    Micro-mass directed ESC differentiation towards the osteoblast lineage. (A) Morphological changes on day 4 of differentiation between the six media conditions tested: FBS-basic (a), FBS-Dex (b), <t>FBS-VD3</t> (c), <t>KSR-basic</t> (d), KSR-Dex (e), KSR-VD3 (f). Scale bars represent 100 µm. (B) Apoptotic cells were observed using TUNEL on day 4 of differentiation in KSR-Dex (b) and KSR-VD3 (d). The corresponding brightfield channels demonstrates cell position (a and c respectively); scale bars represent 100 µm. (C) Re-attached aggregates on day 7 show significant differences at day 7 between the six media types: FBS-basic (a), FBS-Dex (b), FBS-VD3 (c), KSR-basic (d), KSR-Dex (e), KSR-VD3 (f). (D) After trypsinization on day 7 of differentiation, aggregates also show differences between the six media types: FBS-basic (a), FBS-Dex (b), FBS-VD3 (c), KSR-basic (d), KSR-Dex (e), KSR-VD3 (f); scale bars represent 100 µm. (E) Expression of osteoblast-related proteins, COL 1 and osteocalcin using immunofluorescence on day 7 of differentiation: FBS-Dex (a, m), FBS-VD3 (d, p), KSR-Dex (g, s) and KSR-VD3 (j, v). Brightfield (b, e, h, k, n, g, t, w) and DAPI (c, f, i, l, o, r, u, x) are also shown; scale bars represent 50 µm. (F) Using Alizarin Red S staining, calcification with red appearance was observed in culture dish on day 7 and 14 of differentiation: FBS-basic (a, d), FBS-Dex (b, e), FBS-VD3 (c, f), KSR-basic (g, j), KSR-Dex (h, k), KSR-VD3 (i, l); scale bars represent 50 µm. (G) Calcium content per micro-mass spot (a) and normalized against DNA (b) was determined; data is expressed as mean ± SD (n = 3) per well. # represents a significant difference between FBS-Dex and VD3 or KSR-Dex and VD3; P
    Knockout Serum Replacement Ksr, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 943 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher heat inactivated fbs
    Thrombin-derived peptides modulate the cytokine response to LPS in vitro. (A and B) Measurement of nitrite release of RAW 264.7 macrophages stimulated with 10 ng/ml E. coli or P. aeruginosa LPS in combination with the indicated concentrations of GKY25 and HVF18 (n = 3). (C and D) RAW 264.7 cells were stimulated with 10 ng/ml E. coli LPS and cytokines were analysed in the cell supernatants (n = 3). (E and F) Human blood was treated with 10 ng/ml E. coli LPS alone, or with LPS and GKY25 (E) or HVF18 (F). After 6 h of incubation TNF-α was determined in plasma by ELISA (n = 3). (G) Binding of GKY25 and WFF25 to 125I -labeled E. coli LPS using a slot blot assay. (H) Stimulation of RAW 264.7 cells by LPS and the effects of peptides. Left panel: LPS was incubated with GKY25 or WFF25, followed by addition of serum and incubation with the cells. Right panel: Standard procedure as in A. Peptides were added to cells pre-incubated briefly with LPS in <t>DMEM</t> with 10% <t>FBS</t> (n = 3).
    Heat Inactivated Fbs, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 12349 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher rpmi 1640
    Thrombin-derived peptides modulate the cytokine response to LPS in vitro. (A and B) Measurement of nitrite release of RAW 264.7 macrophages stimulated with 10 ng/ml E. coli or P. aeruginosa LPS in combination with the indicated concentrations of GKY25 and HVF18 (n = 3). (C and D) RAW 264.7 cells were stimulated with 10 ng/ml E. coli LPS and cytokines were analysed in the cell supernatants (n = 3). (E and F) Human blood was treated with 10 ng/ml E. coli LPS alone, or with LPS and GKY25 (E) or HVF18 (F). After 6 h of incubation TNF-α was determined in plasma by ELISA (n = 3). (G) Binding of GKY25 and WFF25 to 125I -labeled E. coli LPS using a slot blot assay. (H) Stimulation of RAW 264.7 cells by LPS and the effects of peptides. Left panel: LPS was incubated with GKY25 or WFF25, followed by addition of serum and incubation with the cells. Right panel: Standard procedure as in A. Peptides were added to cells pre-incubated briefly with LPS in <t>DMEM</t> with 10% <t>FBS</t> (n = 3).
    Rpmi 1640, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 109773 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher rnasezap rnase decontamination solution
    Thrombin-derived peptides modulate the cytokine response to LPS in vitro. (A and B) Measurement of nitrite release of RAW 264.7 macrophages stimulated with 10 ng/ml E. coli or P. aeruginosa LPS in combination with the indicated concentrations of GKY25 and HVF18 (n = 3). (C and D) RAW 264.7 cells were stimulated with 10 ng/ml E. coli LPS and cytokines were analysed in the cell supernatants (n = 3). (E and F) Human blood was treated with 10 ng/ml E. coli LPS alone, or with LPS and GKY25 (E) or HVF18 (F). After 6 h of incubation TNF-α was determined in plasma by ELISA (n = 3). (G) Binding of GKY25 and WFF25 to 125I -labeled E. coli LPS using a slot blot assay. (H) Stimulation of RAW 264.7 cells by LPS and the effects of peptides. Left panel: LPS was incubated with GKY25 or WFF25, followed by addition of serum and incubation with the cells. Right panel: Standard procedure as in A. Peptides were added to cells pre-incubated briefly with LPS in <t>DMEM</t> with 10% <t>FBS</t> (n = 3).
    Rnasezap Rnase Decontamination Solution, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 236 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Millipore 6 ohda
    Validation of the rat model of PD and LID. ( A ) Experimental timeline showing <t>6-OHDA</t> lesioning, L -DOPA administration, behavioral testing, and animal grouping. ( B ) Time course of the manifestation of AIMs scored every 3 days over a period of 21 days after the final L -DOPA administration (n = 15). ( C ) Representative photomicrographs of TH immunohistochemical staining in coronal brain sections of the striatum and SN of rats subjected to 6-OHDA injection into the right striatum (PD) with (LID) or without (NLID) L -DOPA administration. Magnified images correspond to labeled boxes in the upper panels (n = 3). ( D ) Quantification of TH expression in the striatum and SN and of c-FOS, p-ERK, and ERK expression in the striatum of PD and LID rats and their corresponding control groups (n = 3–5). The signal intensity of protein bands was normalized to that of GAPDH. ( E ) qRT-PCR detection of c-Fos expression in the striatum of PD and LID rats and their corresponding controls. Data are shown as mean ± SEM (n = 6). **P
    6 Ohda, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 1832 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher hdl cholesterol
    Boxplots showing median values and interquartile ranges of selected blood biomarkers: total cholesterol a <t>HDL</t> cholesterol b , <t>LDL</t> cholesterol ( c ), and TG d in the F1 generation. Ccircles represent outliers that extend more than 1.5 box-lengths from the edge of the box, and the stars represent extreme outliers which extend more than three box-lengths; p: level of significance; NS: non-significant
    Hdl Cholesterol, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 98/100, based on 228 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore histopaque 1077
    Boxplots showing median values and interquartile ranges of selected blood biomarkers: total cholesterol a <t>HDL</t> cholesterol b , <t>LDL</t> cholesterol ( c ), and TG d in the F1 generation. Ccircles represent outliers that extend more than 1.5 box-lengths from the edge of the box, and the stars represent extreme outliers which extend more than three box-lengths; p: level of significance; NS: non-significant
    Histopaque 1077, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 12612 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore dopamine hydrochloride
    Boxplots showing median values and interquartile ranges of selected blood biomarkers: total cholesterol a <t>HDL</t> cholesterol b , <t>LDL</t> cholesterol ( c ), and TG d in the F1 generation. Ccircles represent outliers that extend more than 1.5 box-lengths from the edge of the box, and the stars represent extreme outliers which extend more than three box-lengths; p: level of significance; NS: non-significant
    Dopamine Hydrochloride, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 969 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher triglyceride levels
    Boxplots showing median values and interquartile ranges of selected blood biomarkers: total cholesterol a <t>HDL</t> cholesterol b , <t>LDL</t> cholesterol ( c ), and TG d in the F1 generation. Ccircles represent outliers that extend more than 1.5 box-lengths from the edge of the box, and the stars represent extreme outliers which extend more than three box-lengths; p: level of significance; NS: non-significant
    Triglyceride Levels, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 246 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher sodium pyruvate
    Boxplots showing median values and interquartile ranges of selected blood biomarkers: total cholesterol a <t>HDL</t> cholesterol b , <t>LDL</t> cholesterol ( c ), and TG d in the F1 generation. Ccircles represent outliers that extend more than 1.5 box-lengths from the edge of the box, and the stars represent extreme outliers which extend more than three box-lengths; p: level of significance; NS: non-significant
    Sodium Pyruvate, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 44577 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher tri reagent
    Boxplots showing median values and interquartile ranges of selected blood biomarkers: total cholesterol a <t>HDL</t> cholesterol b , <t>LDL</t> cholesterol ( c ), and TG d in the F1 generation. Ccircles represent outliers that extend more than 1.5 box-lengths from the edge of the box, and the stars represent extreme outliers which extend more than three box-lengths; p: level of significance; NS: non-significant
    Tri Reagent, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 12250 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    IL-17A, IL-22 and proliferative responses from PBMCs obtained from healthy Swedish adults in response to stimulation with pneumococcal antigens. PBMCs were stimulated with the pneumococcal antigens WCA, PdT, PcsB, PsaA, the control antigens PPD and PHA or medium alone (NS) as described in the methods section. Five days after stimulation, the concentrations of IL-17A (A) and IL-22 (B) were measured in culture supernatants and cell proliferation was analyzed (C). Each symbol represents the responses from a single individual. Horizontal lines represent median responses.

    Journal: Vaccine

    Article Title: Characterization of Th17 responses to Streptococcus pneumoniae in humans: comparisons between adults and children in a developed and a developing country

    doi: 10.1016/j.vaccine.2012.03.082

    Figure Lengend Snippet: IL-17A, IL-22 and proliferative responses from PBMCs obtained from healthy Swedish adults in response to stimulation with pneumococcal antigens. PBMCs were stimulated with the pneumococcal antigens WCA, PdT, PcsB, PsaA, the control antigens PPD and PHA or medium alone (NS) as described in the methods section. Five days after stimulation, the concentrations of IL-17A (A) and IL-22 (B) were measured in culture supernatants and cell proliferation was analyzed (C). Each symbol represents the responses from a single individual. Horizontal lines represent median responses.

    Article Snippet: Purified protein derivative of Mycobacterium tuberculosis (PPD) was purchased from Statens Serum Institut (Denmark), phytohemagglutinin (PHA) from Remel (UK) and staphylococcus enterotoxin B (SEB) from Sigma (Germany).

    Techniques:

    The MI was measured in lymphocytes stimulated by each of the seven mitogens and PHA-M alone using different concentrations ( A ) or a combination of selected mitogens with either LPS ( B ) or SLO ( C ). For PHA-L and PHA-M working solutions in microliters of

    Journal: Radiation Protection Dosimetry

    Article Title: Comparing seven mitogens with PHA-M for improved lymphocyte stimulation in dicentric chromosome analysis for biodosimetry

    doi: 10.1093/rpd/ncv286

    Figure Lengend Snippet: The MI was measured in lymphocytes stimulated by each of the seven mitogens and PHA-M alone using different concentrations ( A ) or a combination of selected mitogens with either LPS ( B ) or SLO ( C ). For PHA-L and PHA-M working solutions in microliters of

    Article Snippet: Finally, 100 µl PHA-M (10576-015, Gibco-BRL) and other mitogens (see below) were added in three different concentrations to stimulate lymphocytes.

    Techniques:

    Copy number of mtDNA and its transcription in the peripheral blood from diabetic subjects. ( a ) Copy number was quantified in the genomic DNA by qPCR using CYTB as mtDNA-encoded and β-ACTIN as a nuclear DNA-encoded gene. ( b ) Transcripts of mtDNA-encoded CYTB were quantified in the blood cDNA by qPCR using β-ACTIN as a housekeeping gene. The values are represented as mean ± SD obtained from five to six diabetic patients each with retinopathy (Diab-Ret) or without retinopathy (Diab-No Ret), and 7 to 10 nondiabetic subjects (Norm). * P

    Journal: Investigative Ophthalmology & Visual Science

    Article Title: Peripheral Blood Mitochondrial DNA Damage as a Potential Noninvasive Biomarker of Diabetic Retinopathy

    doi: 10.1167/iovs.16-19073

    Figure Lengend Snippet: Copy number of mtDNA and its transcription in the peripheral blood from diabetic subjects. ( a ) Copy number was quantified in the genomic DNA by qPCR using CYTB as mtDNA-encoded and β-ACTIN as a nuclear DNA-encoded gene. ( b ) Transcripts of mtDNA-encoded CYTB were quantified in the blood cDNA by qPCR using β-ACTIN as a housekeeping gene. The values are represented as mean ± SD obtained from five to six diabetic patients each with retinopathy (Diab-Ret) or without retinopathy (Diab-No Ret), and 7 to 10 nondiabetic subjects (Norm). * P

    Article Snippet: Complementary DNA (cDNA) was synthesized by High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Carlsbad, CA, USA), and transcripts of mtDNA-encoded cytb of complex III and NADPH dehydrogenase 6 (ND6 ) of complex I of the electron transport chain were quantified by SYBR green–based qPCR using β-ACTIN as a housekeeping gene.,

    Techniques: Real-time Polymerase Chain Reaction

    M. corti infection results in increased RNA expression of AAM markers Total RNA was isolated from infected and vehicle control mice brains at 1 wk and 2 wk p.i. using Trizol reagent. Isolated RNA was reversed transcribed to cDNA by using random primers. The mRNA transcript levels of YM1, Fizz1, ARG-1, and iNOS as well as housekeeping genes 18S, beta actin and GAPDH in these samples were measured by Real Time PCR analysis using SYBR green as the detection dye. Expression of each specific gene in infected samples was determined as fold change over that in control samples as calculated by using the formula 2 −(ΔΔCt) (after normalizing with housekeeping genes). The data represent the mean ± SEM of three independent experiments at 1wk p.i. and mean of two independent experiments at 2wk p.i.

    Journal: Journal of neuroimmunology

    Article Title: STAT6−/− mice exhibit decreased cells with alternatively activated macrophage phenotypes and enhanced disease severity in murine neurocysticercosis

    doi: 10.1016/j.jneuroim.2010.09.029

    Figure Lengend Snippet: M. corti infection results in increased RNA expression of AAM markers Total RNA was isolated from infected and vehicle control mice brains at 1 wk and 2 wk p.i. using Trizol reagent. Isolated RNA was reversed transcribed to cDNA by using random primers. The mRNA transcript levels of YM1, Fizz1, ARG-1, and iNOS as well as housekeeping genes 18S, beta actin and GAPDH in these samples were measured by Real Time PCR analysis using SYBR green as the detection dye. Expression of each specific gene in infected samples was determined as fold change over that in control samples as calculated by using the formula 2 −(ΔΔCt) (after normalizing with housekeeping genes). The data represent the mean ± SEM of three independent experiments at 1wk p.i. and mean of two independent experiments at 2wk p.i.

    Article Snippet: Total RNA was extracted using Trizol reagent (Invitrogen) according to manufacturers’ instructions, and cDNA was prepared from 1 µg total RNA using the High Capacity cDNA Archive Kit (Applied Biosystems).

    Techniques: Infection, RNA Expression, Isolation, Mouse Assay, Real-time Polymerase Chain Reaction, SYBR Green Assay, Expressing

    Comparison of matched genomic and cell-line transformed DNA for identified SNPs. Comparison of matched genomic and cell-line transformed DNA for rs141067872, rs10132942 (both miR - 329 - 2 ), rs7521574 and rs112695918 (both miR - 429 ) data generated by the Ion PGM™. The matching gDNA and cell-line transformed DNA show consistent results indicated by the base colour patterns in each example. Chr chromosome, hg human genome

    Journal: BMC Research Notes

    Article Title: Validation of differentially methylated microRNAs identified from an epigenome-wide association study; Sanger and next generation sequencing approaches

    doi: 10.1186/s13104-018-3872-x

    Figure Lengend Snippet: Comparison of matched genomic and cell-line transformed DNA for identified SNPs. Comparison of matched genomic and cell-line transformed DNA for rs141067872, rs10132942 (both miR - 329 - 2 ), rs7521574 and rs112695918 (both miR - 429 ) data generated by the Ion PGM™. The matching gDNA and cell-line transformed DNA show consistent results indicated by the base colour patterns in each example. Chr chromosome, hg human genome

    Article Snippet: Both the Ion 316™ Chip v2 and the Ion 318™ Chip v2 were used to sequence the DNA samples using the Ion PGM™ System (Thermo Fisher Scientific), before the raw data was analysed using Torrent Suite™ Software v4.0.4 and Partek® Genomics Suite® 6.6 software (Partek® Inc., USA).

    Techniques: Transformation Assay, Generated

    Comparison of SNPs located within miR - 329 - 2 and miR - 429 identified by targeted NGS and Sanger sequencing. The data generated by both platforms showed consistent results for SNP calls. Ion PGM™ data analysed using Partek Genomics Suite is shown on the left, with the complementary Sanger sequence results shown on the right, for matching genomic DNA samples. Chr chromosome, DC diabetic control, DKD diabetic kidney disease, hg human genome, Ref reference, Seq sequence

    Journal: BMC Research Notes

    Article Title: Validation of differentially methylated microRNAs identified from an epigenome-wide association study; Sanger and next generation sequencing approaches

    doi: 10.1186/s13104-018-3872-x

    Figure Lengend Snippet: Comparison of SNPs located within miR - 329 - 2 and miR - 429 identified by targeted NGS and Sanger sequencing. The data generated by both platforms showed consistent results for SNP calls. Ion PGM™ data analysed using Partek Genomics Suite is shown on the left, with the complementary Sanger sequence results shown on the right, for matching genomic DNA samples. Chr chromosome, DC diabetic control, DKD diabetic kidney disease, hg human genome, Ref reference, Seq sequence

    Article Snippet: Both the Ion 316™ Chip v2 and the Ion 318™ Chip v2 were used to sequence the DNA samples using the Ion PGM™ System (Thermo Fisher Scientific), before the raw data was analysed using Torrent Suite™ Software v4.0.4 and Partek® Genomics Suite® 6.6 software (Partek® Inc., USA).

    Techniques: Next-Generation Sequencing, Sequencing, Generated

    Workflow by the Ion PGM sequencer (A) and three different nine loci HLA genotyping procedures by PCR and NGS (B) . White and gray boxes indicate experimental steps using either several micro-tubes or a single micro-tube, respectively. Numbers in micro-tubes indicate template DNA amounts (ng).

    Journal: BMC Genomics

    Article Title: Cost-efficient multiplex PCR for routine genotyping of up to nine classical HLA loci in a single analytical run of multiple samples by next generation sequencing

    doi: 10.1186/s12864-015-1514-4

    Figure Lengend Snippet: Workflow by the Ion PGM sequencer (A) and three different nine loci HLA genotyping procedures by PCR and NGS (B) . White and gray boxes indicate experimental steps using either several micro-tubes or a single micro-tube, respectively. Numbers in micro-tubes indicate template DNA amounts (ng).

    Article Snippet: To solve the phase ambiguity problem, we previously reported the development and application of the super high resolution-single molecule-sequence-based typing (SS-SBT) method using long-range PCR of the sample DNA from the promoter-enhancer region to the 3′ untranslated region (3′UTR) for 11 classical HLA loci, HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DRB3/4/5, HLA-DQA1, HLA-DQB1, HLA-DPA1, and HLA-DPB1 in combination with next generation sequencing (NGS) platforms such as Ion PGM (Life Technologies) and GS Junior (Roche) [ - ].

    Techniques: Polymerase Chain Reaction, Next-Generation Sequencing

    NGS workflow used for different Ion Torrent platforms in a clinical laboratory. Ion PGM, Ion Proton and Ion S5XL sequencing workflow using cancer hot spot panel v2 (CHPv2), oncomine panel (OCP) and comprehensive cancer panel (CCP) for library prep. Ion one touch 2 and Ion one touch ES was used for PGM and Proton for template preparation and enrichment of ion spheres. Enriched ion spheres were sequenced on Ion PGM and Ion Proton respectively. For Ion S5XL Ion chef was used which automates the template preparation, enrichment and chip loading. Preloaded reagent cartridge and on board Torrent suite software reduces the initialization, sequencing and data analysis time.

    Journal: PLoS ONE

    Article Title: Versatile ion S5XL sequencer for targeted next generation sequencing of solid tumors in a clinical laboratory

    doi: 10.1371/journal.pone.0181968

    Figure Lengend Snippet: NGS workflow used for different Ion Torrent platforms in a clinical laboratory. Ion PGM, Ion Proton and Ion S5XL sequencing workflow using cancer hot spot panel v2 (CHPv2), oncomine panel (OCP) and comprehensive cancer panel (CCP) for library prep. Ion one touch 2 and Ion one touch ES was used for PGM and Proton for template preparation and enrichment of ion spheres. Enriched ion spheres were sequenced on Ion PGM and Ion Proton respectively. For Ion S5XL Ion chef was used which automates the template preparation, enrichment and chip loading. Preloaded reagent cartridge and on board Torrent suite software reduces the initialization, sequencing and data analysis time.

    Article Snippet: Mutations (n = 241) in a number of genes were identified in the tumor tissues using the Ion Ampliseq Cancer Hotspot Panel V2 on the Ion PGM platform and the OCP and CCP on Ion Proton were compared.

    Techniques: Next-Generation Sequencing, Sequencing, Chromatin Immunoprecipitation, Software

    Micro-mass directed ESC differentiation towards the osteoblast lineage. (A) Morphological changes on day 4 of differentiation between the six media conditions tested: FBS-basic (a), FBS-Dex (b), FBS-VD3 (c), KSR-basic (d), KSR-Dex (e), KSR-VD3 (f). Scale bars represent 100 µm. (B) Apoptotic cells were observed using TUNEL on day 4 of differentiation in KSR-Dex (b) and KSR-VD3 (d). The corresponding brightfield channels demonstrates cell position (a and c respectively); scale bars represent 100 µm. (C) Re-attached aggregates on day 7 show significant differences at day 7 between the six media types: FBS-basic (a), FBS-Dex (b), FBS-VD3 (c), KSR-basic (d), KSR-Dex (e), KSR-VD3 (f). (D) After trypsinization on day 7 of differentiation, aggregates also show differences between the six media types: FBS-basic (a), FBS-Dex (b), FBS-VD3 (c), KSR-basic (d), KSR-Dex (e), KSR-VD3 (f); scale bars represent 100 µm. (E) Expression of osteoblast-related proteins, COL 1 and osteocalcin using immunofluorescence on day 7 of differentiation: FBS-Dex (a, m), FBS-VD3 (d, p), KSR-Dex (g, s) and KSR-VD3 (j, v). Brightfield (b, e, h, k, n, g, t, w) and DAPI (c, f, i, l, o, r, u, x) are also shown; scale bars represent 50 µm. (F) Using Alizarin Red S staining, calcification with red appearance was observed in culture dish on day 7 and 14 of differentiation: FBS-basic (a, d), FBS-Dex (b, e), FBS-VD3 (c, f), KSR-basic (g, j), KSR-Dex (h, k), KSR-VD3 (i, l); scale bars represent 50 µm. (G) Calcium content per micro-mass spot (a) and normalized against DNA (b) was determined; data is expressed as mean ± SD (n = 3) per well. # represents a significant difference between FBS-Dex and VD3 or KSR-Dex and VD3; P

    Journal: PLoS ONE

    Article Title: Microenvironment Modulates Osteogenic Cell Lineage Commitment in Differentiated Embryonic Stem Cells

    doi: 10.1371/journal.pone.0009663

    Figure Lengend Snippet: Micro-mass directed ESC differentiation towards the osteoblast lineage. (A) Morphological changes on day 4 of differentiation between the six media conditions tested: FBS-basic (a), FBS-Dex (b), FBS-VD3 (c), KSR-basic (d), KSR-Dex (e), KSR-VD3 (f). Scale bars represent 100 µm. (B) Apoptotic cells were observed using TUNEL on day 4 of differentiation in KSR-Dex (b) and KSR-VD3 (d). The corresponding brightfield channels demonstrates cell position (a and c respectively); scale bars represent 100 µm. (C) Re-attached aggregates on day 7 show significant differences at day 7 between the six media types: FBS-basic (a), FBS-Dex (b), FBS-VD3 (c), KSR-basic (d), KSR-Dex (e), KSR-VD3 (f). (D) After trypsinization on day 7 of differentiation, aggregates also show differences between the six media types: FBS-basic (a), FBS-Dex (b), FBS-VD3 (c), KSR-basic (d), KSR-Dex (e), KSR-VD3 (f); scale bars represent 100 µm. (E) Expression of osteoblast-related proteins, COL 1 and osteocalcin using immunofluorescence on day 7 of differentiation: FBS-Dex (a, m), FBS-VD3 (d, p), KSR-Dex (g, s) and KSR-VD3 (j, v). Brightfield (b, e, h, k, n, g, t, w) and DAPI (c, f, i, l, o, r, u, x) are also shown; scale bars represent 50 µm. (F) Using Alizarin Red S staining, calcification with red appearance was observed in culture dish on day 7 and 14 of differentiation: FBS-basic (a, d), FBS-Dex (b, e), FBS-VD3 (c, f), KSR-basic (g, j), KSR-Dex (h, k), KSR-VD3 (i, l); scale bars represent 50 µm. (G) Calcium content per micro-mass spot (a) and normalized against DNA (b) was determined; data is expressed as mean ± SD (n = 3) per well. # represents a significant difference between FBS-Dex and VD3 or KSR-Dex and VD3; P

    Article Snippet: To the base medium the following factors were added (i) FBS-basic: 15% FBS (Invitrogen), (ii) FBS-Dex: 15% FBS, 50 µg/ml Ascorbic acid (AA) (Sigma), 10 mM β-glycerophosphate (β-GP) (Sigma), 100 nM dexamethasone (Dex) (Sigma), (iii) FBS-VD3: 15% FBS, 50 µg/ml AA, 10 mM β-GP, 50 nM 1,25-OH2 Vitamin D3 (VD3) (Calbiochem). (iv) KSR-basic: 15% Knockout Serum Replacement (KSR) (Invitrogen), (v) KSR-Dex: 15% KSR, 50 µg/ml AA, 10 mM β-GP, 100 nM Dex (vi) KSR-VD3: 15% KSR, 50 µg/ml AA, 10 mM β-GP, 50 nM VD3.

    Techniques: TUNEL Assay, Expressing, Immunofluorescence, Staining

    Trapped, undifferentiated and differentiated ESCs within aggregates in stirred suspension culture. (A) ESC-derived aggregates displayed dramatic changes in morphology in static and stirred suspension culture using KSR-VD3 medium: micro-mass (a, b), static suspension (c-l), stirred suspension (m-v); scale bars represent 100 µm. (B) The average area of aggregates in a static or stirred suspension culture was determined during culture; data is expressed as means ± SD (n = 10) per lane. # represents a significant difference between static and stirred suspension; P

    Journal: PLoS ONE

    Article Title: Microenvironment Modulates Osteogenic Cell Lineage Commitment in Differentiated Embryonic Stem Cells

    doi: 10.1371/journal.pone.0009663

    Figure Lengend Snippet: Trapped, undifferentiated and differentiated ESCs within aggregates in stirred suspension culture. (A) ESC-derived aggregates displayed dramatic changes in morphology in static and stirred suspension culture using KSR-VD3 medium: micro-mass (a, b), static suspension (c-l), stirred suspension (m-v); scale bars represent 100 µm. (B) The average area of aggregates in a static or stirred suspension culture was determined during culture; data is expressed as means ± SD (n = 10) per lane. # represents a significant difference between static and stirred suspension; P

    Article Snippet: To the base medium the following factors were added (i) FBS-basic: 15% FBS (Invitrogen), (ii) FBS-Dex: 15% FBS, 50 µg/ml Ascorbic acid (AA) (Sigma), 10 mM β-glycerophosphate (β-GP) (Sigma), 100 nM dexamethasone (Dex) (Sigma), (iii) FBS-VD3: 15% FBS, 50 µg/ml AA, 10 mM β-GP, 50 nM 1,25-OH2 Vitamin D3 (VD3) (Calbiochem). (iv) KSR-basic: 15% Knockout Serum Replacement (KSR) (Invitrogen), (v) KSR-Dex: 15% KSR, 50 µg/ml AA, 10 mM β-GP, 100 nM Dex (vi) KSR-VD3: 15% KSR, 50 µg/ml AA, 10 mM β-GP, 50 nM VD3.

    Techniques: Derivative Assay

    Adipogenesis during ESC osteoblast differentiation in static culture. (A) Using Oil Red O staining, lipids with dark red appearance were observed in re-attached cells on day 10 of differentiation in static: KSR-basic (a), KSR-Dex (b), KSR-VD3 (c). Oil Red O co-staining with Alizarin Red S shows both lipid and calcification within re-attached cells in KSR-Dex (d) and KSR-VD3 (e); scale bars represent 20 µm. (B) Lipid accumulation per micro-mass spot was determined on day 10 of differentiation (a). Lipid accumulation was also normalized against DNA content to determine lipid synthesis per cell (b); data is expressed as mean ± SD (n = 3) per well. * represents a significant difference between undifferentiated and differentiated ESCs; P

    Journal: PLoS ONE

    Article Title: Microenvironment Modulates Osteogenic Cell Lineage Commitment in Differentiated Embryonic Stem Cells

    doi: 10.1371/journal.pone.0009663

    Figure Lengend Snippet: Adipogenesis during ESC osteoblast differentiation in static culture. (A) Using Oil Red O staining, lipids with dark red appearance were observed in re-attached cells on day 10 of differentiation in static: KSR-basic (a), KSR-Dex (b), KSR-VD3 (c). Oil Red O co-staining with Alizarin Red S shows both lipid and calcification within re-attached cells in KSR-Dex (d) and KSR-VD3 (e); scale bars represent 20 µm. (B) Lipid accumulation per micro-mass spot was determined on day 10 of differentiation (a). Lipid accumulation was also normalized against DNA content to determine lipid synthesis per cell (b); data is expressed as mean ± SD (n = 3) per well. * represents a significant difference between undifferentiated and differentiated ESCs; P

    Article Snippet: To the base medium the following factors were added (i) FBS-basic: 15% FBS (Invitrogen), (ii) FBS-Dex: 15% FBS, 50 µg/ml Ascorbic acid (AA) (Sigma), 10 mM β-glycerophosphate (β-GP) (Sigma), 100 nM dexamethasone (Dex) (Sigma), (iii) FBS-VD3: 15% FBS, 50 µg/ml AA, 10 mM β-GP, 50 nM 1,25-OH2 Vitamin D3 (VD3) (Calbiochem). (iv) KSR-basic: 15% Knockout Serum Replacement (KSR) (Invitrogen), (v) KSR-Dex: 15% KSR, 50 µg/ml AA, 10 mM β-GP, 100 nM Dex (vi) KSR-VD3: 15% KSR, 50 µg/ml AA, 10 mM β-GP, 50 nM VD3.

    Techniques: Staining

    Bone-like tissue formation in vitro and in vivo . (A) The ultra-structure of aggregates was analyzed by SEM on day 15 of stirred suspension culture: KSR-basic (a, d), KSR-Dex (b, e), KSR-VD3 (c, f). Low magnification (a, b, c), scale bars represent 50 µm; high magnification (d, e, f), scale bars represent 10 µm. (B) Histological sections of aggregates were analyzed by hematoxylin and eosin (H E) staining after 15 days of differentiation: KSR-basic (a), KSR-Dex (b), KSR-VD3 (c); scale bars represent 20 µm. (C) Expression of osteoblast-related mRNAs (Cbfa1, osteocalcin) was analyzed using real-time PCR during ESC differentiation in KSR-VD3 static suspension culture. (D) Calcium content was analyzed during ESC differentiation in KSR-VD3 static suspension culture and normalized against DNA content. (E) Expression of adipocyte-related mRNAs (PPARγ, aP2) was analyzed using real-time RT-PCR during ESC differentiation in KSR-VD3 static suspension culture; data is expressed as means ± SD (n = 3) per lane. * represents a significant difference between two conditions tested; P

    Journal: PLoS ONE

    Article Title: Microenvironment Modulates Osteogenic Cell Lineage Commitment in Differentiated Embryonic Stem Cells

    doi: 10.1371/journal.pone.0009663

    Figure Lengend Snippet: Bone-like tissue formation in vitro and in vivo . (A) The ultra-structure of aggregates was analyzed by SEM on day 15 of stirred suspension culture: KSR-basic (a, d), KSR-Dex (b, e), KSR-VD3 (c, f). Low magnification (a, b, c), scale bars represent 50 µm; high magnification (d, e, f), scale bars represent 10 µm. (B) Histological sections of aggregates were analyzed by hematoxylin and eosin (H E) staining after 15 days of differentiation: KSR-basic (a), KSR-Dex (b), KSR-VD3 (c); scale bars represent 20 µm. (C) Expression of osteoblast-related mRNAs (Cbfa1, osteocalcin) was analyzed using real-time PCR during ESC differentiation in KSR-VD3 static suspension culture. (D) Calcium content was analyzed during ESC differentiation in KSR-VD3 static suspension culture and normalized against DNA content. (E) Expression of adipocyte-related mRNAs (PPARγ, aP2) was analyzed using real-time RT-PCR during ESC differentiation in KSR-VD3 static suspension culture; data is expressed as means ± SD (n = 3) per lane. * represents a significant difference between two conditions tested; P

    Article Snippet: To the base medium the following factors were added (i) FBS-basic: 15% FBS (Invitrogen), (ii) FBS-Dex: 15% FBS, 50 µg/ml Ascorbic acid (AA) (Sigma), 10 mM β-glycerophosphate (β-GP) (Sigma), 100 nM dexamethasone (Dex) (Sigma), (iii) FBS-VD3: 15% FBS, 50 µg/ml AA, 10 mM β-GP, 50 nM 1,25-OH2 Vitamin D3 (VD3) (Calbiochem). (iv) KSR-basic: 15% Knockout Serum Replacement (KSR) (Invitrogen), (v) KSR-Dex: 15% KSR, 50 µg/ml AA, 10 mM β-GP, 100 nM Dex (vi) KSR-VD3: 15% KSR, 50 µg/ml AA, 10 mM β-GP, 50 nM VD3.

    Techniques: In Vitro, In Vivo, Staining, Expressing, Real-time Polymerase Chain Reaction, Quantitative RT-PCR

    Thrombin-derived peptides modulate the cytokine response to LPS in vitro. (A and B) Measurement of nitrite release of RAW 264.7 macrophages stimulated with 10 ng/ml E. coli or P. aeruginosa LPS in combination with the indicated concentrations of GKY25 and HVF18 (n = 3). (C and D) RAW 264.7 cells were stimulated with 10 ng/ml E. coli LPS and cytokines were analysed in the cell supernatants (n = 3). (E and F) Human blood was treated with 10 ng/ml E. coli LPS alone, or with LPS and GKY25 (E) or HVF18 (F). After 6 h of incubation TNF-α was determined in plasma by ELISA (n = 3). (G) Binding of GKY25 and WFF25 to 125I -labeled E. coli LPS using a slot blot assay. (H) Stimulation of RAW 264.7 cells by LPS and the effects of peptides. Left panel: LPS was incubated with GKY25 or WFF25, followed by addition of serum and incubation with the cells. Right panel: Standard procedure as in A. Peptides were added to cells pre-incubated briefly with LPS in DMEM with 10% FBS (n = 3).

    Journal: PLoS ONE

    Article Title: Host Defense Peptides of Thrombin Modulate Inflammation and Coagulation in Endotoxin-Mediated Shock and Pseudomonas aeruginosa Sepsis

    doi: 10.1371/journal.pone.0051313

    Figure Lengend Snippet: Thrombin-derived peptides modulate the cytokine response to LPS in vitro. (A and B) Measurement of nitrite release of RAW 264.7 macrophages stimulated with 10 ng/ml E. coli or P. aeruginosa LPS in combination with the indicated concentrations of GKY25 and HVF18 (n = 3). (C and D) RAW 264.7 cells were stimulated with 10 ng/ml E. coli LPS and cytokines were analysed in the cell supernatants (n = 3). (E and F) Human blood was treated with 10 ng/ml E. coli LPS alone, or with LPS and GKY25 (E) or HVF18 (F). After 6 h of incubation TNF-α was determined in plasma by ELISA (n = 3). (G) Binding of GKY25 and WFF25 to 125I -labeled E. coli LPS using a slot blot assay. (H) Stimulation of RAW 264.7 cells by LPS and the effects of peptides. Left panel: LPS was incubated with GKY25 or WFF25, followed by addition of serum and incubation with the cells. Right panel: Standard procedure as in A. Peptides were added to cells pre-incubated briefly with LPS in DMEM with 10% FBS (n = 3).

    Article Snippet: RAW 264.7 cells were cultured in Dulbecco's modified Eagle medium (DMEM; PAA-Laboratories) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS) (Invitrogen) and 1% (v/v) Antibiotic-Antimycotic solution (AAS) (Invitrogen).

    Techniques: Derivative Assay, In Vitro, Incubation, Enzyme-linked Immunosorbent Assay, Binding Assay, Labeling, Slot Blot Assay

    Validation of the rat model of PD and LID. ( A ) Experimental timeline showing 6-OHDA lesioning, L -DOPA administration, behavioral testing, and animal grouping. ( B ) Time course of the manifestation of AIMs scored every 3 days over a period of 21 days after the final L -DOPA administration (n = 15). ( C ) Representative photomicrographs of TH immunohistochemical staining in coronal brain sections of the striatum and SN of rats subjected to 6-OHDA injection into the right striatum (PD) with (LID) or without (NLID) L -DOPA administration. Magnified images correspond to labeled boxes in the upper panels (n = 3). ( D ) Quantification of TH expression in the striatum and SN and of c-FOS, p-ERK, and ERK expression in the striatum of PD and LID rats and their corresponding control groups (n = 3–5). The signal intensity of protein bands was normalized to that of GAPDH. ( E ) qRT-PCR detection of c-Fos expression in the striatum of PD and LID rats and their corresponding controls. Data are shown as mean ± SEM (n = 6). **P

    Journal: Aging (Albany NY)

    Article Title: Integrated transcriptome expression profiling reveals a novel lncRNA associated with L-DOPA-induced dyskinesia in a rat model of Parkinson’s disease

    doi: 10.18632/aging.102652

    Figure Lengend Snippet: Validation of the rat model of PD and LID. ( A ) Experimental timeline showing 6-OHDA lesioning, L -DOPA administration, behavioral testing, and animal grouping. ( B ) Time course of the manifestation of AIMs scored every 3 days over a period of 21 days after the final L -DOPA administration (n = 15). ( C ) Representative photomicrographs of TH immunohistochemical staining in coronal brain sections of the striatum and SN of rats subjected to 6-OHDA injection into the right striatum (PD) with (LID) or without (NLID) L -DOPA administration. Magnified images correspond to labeled boxes in the upper panels (n = 3). ( D ) Quantification of TH expression in the striatum and SN and of c-FOS, p-ERK, and ERK expression in the striatum of PD and LID rats and their corresponding control groups (n = 3–5). The signal intensity of protein bands was normalized to that of GAPDH. ( E ) qRT-PCR detection of c-Fos expression in the striatum of PD and LID rats and their corresponding controls. Data are shown as mean ± SEM (n = 6). **P

    Article Snippet: 6-OHDA lesioning, L -DOPA administration, and behavioral testing Rats were unilaterally lesioned by injection of 6-OHDA (12 μg/2.4 μl; Sigma-Aldrich, St. Louis, MO, USA) into the medial forebrain bundle (3.6 mm posterior and 8.2 mm ventral to bregma and 1.8 mm lateral to the midline) using a Hamilton syringe after anesthetization with 2%–3% isoflurane through an animal anesthesia ventilator system (RWD Life Science Co., Shenzhen, China).

    Techniques: Immunohistochemistry, Staining, Injection, Labeling, Expressing, Quantitative RT-PCR

    Boxplots showing median values and interquartile ranges of selected blood biomarkers: total cholesterol a HDL cholesterol b , LDL cholesterol ( c ), and TG d in the F1 generation. Ccircles represent outliers that extend more than 1.5 box-lengths from the edge of the box, and the stars represent extreme outliers which extend more than three box-lengths; p: level of significance; NS: non-significant

    Journal: BMC Genetics

    Article Title: Prenatal caloric restriction alters lipid metabolism but not hepatic Fasn gene expression and methylation profiles in rats

    doi: 10.1186/s12863-017-0544-0

    Figure Lengend Snippet: Boxplots showing median values and interquartile ranges of selected blood biomarkers: total cholesterol a HDL cholesterol b , LDL cholesterol ( c ), and TG d in the F1 generation. Ccircles represent outliers that extend more than 1.5 box-lengths from the edge of the box, and the stars represent extreme outliers which extend more than three box-lengths; p: level of significance; NS: non-significant

    Article Snippet: Concentrations of serum total cholesterol, LDL cholesterol, HDL cholesterol, and triglycerides (TG) were analyzed using commercial kits (Thermo Fisher Scientific, Waltham, MA, USA) and standard enzymatic methods with a Konelab 20i fully automated analyzer (Thermo Electron Corporation, Vantaa, Finland).

    Techniques:

    Boxplots showing median values and interquartile ranges of selected blood biomarkers: total cholesterol a HDL cholesterol b , LDL cholesterol c , and TG d in the F0 generation. Circles represent outliers that extend more than 1.5 box-lengths from the edge of the box, and stars represent extreme outliers that extend more than three box-lengths; p: level of significance; NS: not significant

    Journal: BMC Genetics

    Article Title: Prenatal caloric restriction alters lipid metabolism but not hepatic Fasn gene expression and methylation profiles in rats

    doi: 10.1186/s12863-017-0544-0

    Figure Lengend Snippet: Boxplots showing median values and interquartile ranges of selected blood biomarkers: total cholesterol a HDL cholesterol b , LDL cholesterol c , and TG d in the F0 generation. Circles represent outliers that extend more than 1.5 box-lengths from the edge of the box, and stars represent extreme outliers that extend more than three box-lengths; p: level of significance; NS: not significant

    Article Snippet: Concentrations of serum total cholesterol, LDL cholesterol, HDL cholesterol, and triglycerides (TG) were analyzed using commercial kits (Thermo Fisher Scientific, Waltham, MA, USA) and standard enzymatic methods with a Konelab 20i fully automated analyzer (Thermo Electron Corporation, Vantaa, Finland).

    Techniques: